One idea could be that Batman visits Smallville to investigate some strange technology that has been showing up in Gotham and has ties to LuthorCorp. He teams up with Clark Kent, who is still in his early days of understanding his powers. They could have a cool dynamic where Batman is initially suspicious of Clark but then realizes he's a powerful ally.
Perhaps there's a villain who is using kryptonite in a new way that affects both Gotham and Smallville. Batman, with his detective skills, and Clark, with his superpowers, have to work together to stop this threat. For example, the villain could be creating a device that spreads kryptonite - laced gas, and Batman helps Clark find a way to neutralize it while Clark protects Batman from the villains' minions.
Another plot could involve a time - travel element. Maybe a device in LuthorCorp accidentally sends Batman back in time to when Clark is a teenager in Smallville. Batman has to figure out how to get back to his own time while also helping Clark deal with some local bullies who are actually working for a bigger, more dangerous criminal organization that has ties to Gotham.
Well, a cool plot could be that an ancient, powerful entity from the Supernatural world is awakened in Smallville. Clark discovers it while trying to protect the town. He realizes he can't handle it alone and contacts Bobby Singer through some means. Bobby then sends Sam and Dean to help. They initially have a hard time trusting Clark because of his superpowers, but soon realize they need his help. As they battle the entity, they discover it has ties to an old, forgotten lore that involves both the kryptonite on Earth and a powerful demon they once fought. They have to combine their knowledge and powers to defeat it.
One idea could be that Chloe discovers a hidden power in Smallville that is linked to her own family's past. Maybe she stumbles upon an old diary in the Kent barn that reveals secrets about a long - forgotten relative who had a connection to an otherworldly force in Smallville. This could lead to her and Clark teaming up to uncover more about this mystery and protect Smallville from a new threat that is drawn to this newly - discovered power.
One idea could be that the alien technology from Roswell somehow finds its way to Smallville. The kryptonite in Smallville could have an unexpected reaction with the alien biology from Roswell. Maybe the characters from Roswell come to Smallville in search of a new energy source and end up getting involved with the local mysteries and the Kents.
Perhaps there could be a story where Lex Luthor somehow gets hold of some of Arrow's technology and Clark has to work with Oliver to retrieve it. They would have to combine their skills, Clark's superpowers and Oliver's archery and combat expertise.
Perhaps in the fanfiction, there's a time - traveling aspect. Barry's time - traveling experiments go wrong and he ends up in Smallville during Clark's high school years. They have to figure out how to get Barry back to his own time while also dealing with a villain who is trying to change the future by targeting Clark in the past. This could involve both of them learning about each other's powers and how to work together effectively.
One idea could be that the kryptonite in Smallville starts to affect the mutants in strange ways. Maybe it suppresses or enhances their powers in unexpected manners. For example, Wolverine's healing factor could be slowed down by kryptonite exposure, leading to a real threat when he gets injured. Another plot could involve Lex Luthor getting his hands on some mutant DNA and trying to create his own super - soldiers, which would draw the attention of the X - Men. They could team up with Clark Kent to stop Luthor's evil plans.
One idea could be that the Winchesters end up in Smallville while hunting a demon that has some connection to LuthorCorp's experiments. Maybe the demon is using the kryptonite there for its evil deeds. Another could be that Clark Kent discovers the existence of the supernatural world through Sam and Dean. He could initially be skeptical but then realize there are threats that even his powers might not be enough to handle.
One idea could be that the Flash has to help Batman track down a super - villain who has the ability to manipulate time. Since the Flash is a speedster, he can move through time - altered situations more easily. Another plot could involve Batman creating a new gadget to counter a meta - human threat, and the Flash accidentally gets caught in its test run, causing some wacky time - space anomalies that they have to work together to fix.
A plot could be that Joker gets his hands on a powerful and mischievous Pokemon like Ditto. He uses Ditto to create chaos by transforming into various threats. Batman has to team up with a young Pokemon trainer to stop the Joker. The trainer could introduce Batman to different Pokemon strategies along the way.
Here's an idea. There could be a powerful magical artifact that surfaces in both cities. It has the power to change reality. Superman, being a man of science, is initially skeptical about its power. Batman, on the other hand, has seen enough strange things in Gotham to know it's dangerous. They have to overcome their differences in beliefs as they race against time to stop different factions in both cities who want to use the artifact for their own gain. Along the way, they also learn more about each other's worlds and form a stronger bond.